Colletotrichum gloeosporioides

Wang, Qiu-Tong, Liu, Xiao-Ting, Ma, Hai-Ying, Shen, Xiao-Ye & Hou, Cheng-Lin, 2019, Colletotrichum yulongense sp. nov. and C. rhombiforme isolated as endophytes from Vaccinium dunalianum var. urophyllum in China, Phytotaxa 394 (4), pp. 285-298 : 290

C. gloeosporioides species complex

The phylogram ( Fig. 2 ) shows the identified isolates in the C. gloeosporioides species complex. The combined aligned data matrix (ACT, CAL, CHS-1, GAPDH, ITS, TUB2 and GS) contained 45 isolates including the outgroup ( C. boninense MAFF 305972* and C. hippeastri CBS 241.78*). Forty-three reference sequences were downloaded from GenBank ( Table 1) and two isolates were obtained from V. dunalianum var. urophyllum in this study. The multi-gene dataset (gene boundaries of ACT: 1-275, CAL: 276-1008, CHS-1: 1009-1339, GAPDH: 1340-1581, ITS: 1582-2151, TUB2: 2152-2741 and GS: 2742-3522) comprised 3522 characters including the alignment gaps, of which 656 were parsimony-informative, 485 parsimony-uninformative and 2381 constant. The MP analysis of sequences resulted in one most parsimonious tree ( Fig. 2 ) with a length (TL) of 1914 steps, consistency index (CI) of 0.730, retention index (RI) of 0.810 and homoplasy index (HI) of 0.270. For the Bayesian analysis, MrModeltest 2.3 with the Akaike information criterion (AIC) was used to choose a substitution model for the two datasets. The model GRT+ I + G were chosen for the combined sequences. The analyses of the final MCMC chains were run from random trees for 1,000,000 generations and sampled every 100 generations. The tree generated from Bayesian analysis confirmed the tree topology obtained with parsimony. Two isolates clustered with C. henanense and formed a distinct clade with a high bootstrap support/posterior probability value (bootstrap support BS> 70 and Bayesian posterior probabilities PP> 0.95). A pairwise homoplasy index (PHI) test using a seven-gene dataset (ACT, CAL, CHS-1, GAPDH, ITS, TUB2 and GS) was further performed to determine the recombination level between C. yulongense and its phylogenetically closely related species, C. henanense . The PHI test did not find statistically significant evidence for recombination (Φw = 1). Based on the result no significant recombination events could be detected between C. yulongense and C. henanense ( Fig. 3 ).

Figures

FIGURE 2. Phylogenetic tree derived from maximum parsimony analysis of the combined ACT, CAL, CHS-1, GAPDH, ITS, TUB2 and GS genes of C. gloeosporioides species complex, using C. boninense MAFF 305972* and C. hippeastri CBS 241.78* as outgroups. Bootstrap values of more than 70 from 1000 replications are shown above the respective branches. Bayesian posterior probabilities (PP) were estimated and clades with PP> 0.95 are marked under the branches. The new species, Colletotrichum yulongense, is in bold.

FIGURE 3. Result of the pairwise homoplasy index (PHI) test of closely related species using both LogDet transformation and splits decomposition. PHI test results (Φ w) <0.05 indicate significant recombination within the dataset.